Is supplicating in Qunoot, at times of affliction, during obligatory and voluntary prayer a Sunnah, and should it be done before Rukoo` (bowing), or after it?

At times of affliction, it is a Sunnah that Muslims supplicate in Qunoot after the final Rukoo` of each obligatory, or voluntary prayer as individuals, or in congregation.

Is it permissible to thin the eyebrows or remove them and draw in their place?

Thinning the eyebrows, removing them, and drawing in their place—known as Namas—is prohibited. The Prophet (peace be upon him) cursed those who do it. And Allah Knows Best.

How many Rak`ahs (unit of prayer) are offered in Witr prayer?

All perfect praise be to Allah, The Lord of The Worlds                                                                                                                                                                  Witr (an odd number prayer performed between Isha`a and Fajr) is offered with a minimum of one Rak`ah, and a maximum of eleven, but offering three Rak`ahs is the minimum of its complete form. And Allah Knows Best.

What is the ruling on staring at the Holy Ka'abah?

All perfecy praise be to Allah, The Lord of The Worlds and may His Peace and Blessings be upon our Prophet Muhammad and upon all of his family and companions.

Staring/looking at the Holy Ka'abah is an act of worship even if this took place while performing a prayer, since Al-Baihaqee stated that the Prophet (PBUH) said: " Staring at the Holy Ka'abah is an act of devotion." [Sho'aab Al-Imaan]. And Allah Knows Best.